First International Workshop on Virtual and Augmented Reality dedicated to Molecular Science (VARMS 2015)

Next week, i will attend the 1st International Workshop on Virtual and Augmented Reality dedicated to Molecular Science (VARMS 2015):

The international IEEE Virtual Reality 2015 conference, through the VARMS workshop, gives researchers an excellent opportunity to:

  • keep up to date with new approaches at the interface between Augmented and Virtual Reality, 3D User Interfaces and Video Games to popularize Molecular Science, both in research and teaching contexts,
  • identify efforts to support the deeper integration of Virtual Reality techniques in the processes and practices of research laboratories and companies in the Molecular Science field, promoting the usefulness and usability of Virtual and Augmented Reality in Molecular Science, implying deep ergonomic analyses and user evaluations in the targeted field,
  • highlight convincing success stories, thereby catalysing the use of Virtual and Augmented Reality in the targeted community, as actual research achievements that lead to decisive results in Molecular Science are still rare.

Here is my poster on Assemble2.

poster varms

Use the mfold web server directly from Assemble2

Here is the last feature i have implemented for the upcoming Assemble2 1.2. We will start with an RNA secondary structure displayed in Assemble2 (and predicted from the sequence stored in the sample file ft3100_from_FANTOM3_project.fasta). I have selected the prediction from the algorithm RNAfold.

ft3100_from_FANTOM3_project_fasta_et_New_Post_—_WordPress_com

Now I would like to submit this sequence to the mfold Web server. By choosing Plugins | mfold Web Server, this opens the RNA folding form inside Assemble2. Once the web page loaded, and if a secondary structure is displayed, the name and the sequence are automatically filled in the form.

mfold_Web_Server_et_ft3100_from_FANTOM3_project_fasta

Once the button “Fold RNA” clicked, the sequence is reformatted by the website, indicating that the prediction has been correctly submitted. I have observed that the website is a little bit less reactive through Assemble2, but nothing dramatical. After a while, you should get the predictions. They’re listed on the web page (the blue arrow in the next screen capture), and Assemble2 lists them also in a choice box (the red arrow in the next screen capture).

mfold_Web_Server_et_ft3100_from_FANTOM3_project_fasta

Now i can use this choice box to select the prediction/structure #5 (for example) to see and manipulate it in Assemble2. To do so, i click on the button on the right (the red arrow in the next screen capture). And it’s done!!

Structure__5predicted_from_mfold_et_mfold_Web_Server

To resume, starting from Assemble2 1.2, you will be able to use all the options available from the mfold web server to predict and manipulate your favorite molecule without leaving Assemble2. As you can imagine, more will come, based on the same principle.

Load data directly from RNA databases into Assemble2.

Thanks to JavaFX, the upcoming release of Assemble2 will provide you the way to load data directly from several RNA databases (i have started with the Nucleic Acid Database and RNACentral). You will be able to browse the website as you were used to it. Once on a webpage describing a 3D structure (for the Nucleic Acid Database) or a sequence (for RNACentral), a button will be activated, indicating the ability to import the data into Assemble2.

RNACentral_linked_to_Assemble2